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space for a promoter when changing direction?

Link to this post \| posted 05 Sep, 2019 19:30
NWCiowaSEAPHAGE	We are annotating a B Cluster phage with no subcluster. We have a reverse gene whose start site we'd like to call (to capture all CP) doesn't leave room for a promoter even though it is a reverse gene in a sea of forwards (it is a ~25 bp overlap). Other similar phages also leave no room for a promoter in this region of the genome. I'd love to get some of your thoughts on calling a start to include all CP but leave no room for a change of direction promoter.

Link to this post | posted 05 Sep, 2019 19:30

NWCiowaSEAPHAGE

We are annotating a B Cluster phage with no subcluster. We have a reverse gene whose start site we'd like to call (to capture all CP) doesn't leave room for a promoter even though it is a reverse gene in a sea of forwards (it is a ~25 bp overlap). Other similar phages also leave no room for a promoter in this region of the genome. I'd love to get some of your thoughts on calling a start to include all CP but leave no room for a change of direction promoter.

Link to this post \| posted 15 Oct, 2019 15:42
welkin	while not the usual case, there are a few genes through the Actinobacteriophages that are oriented as you describe. So if it is conserved throughout the cluster, go ahead and call it.